Ginkgo Bioworkshttps://www.ginkgobioworks.com
The Organism CompanyTue, 07 May 2019 13:24:02 +0000en-US
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1 https://wordpress.org/?v=5.2.1Reviving the Smell of Extinct Plantshttps://www.ginkgobioworks.com/2019/05/03/reviving-the-smell-of-extinct-plants/
Fri, 03 May 2019 18:30:58 +0000https://www.ginkgobioworks.com/?p=3427Could we bring back the smell of an extinct flower? Five years ago, this question started us off on an unexpected adventure that’s led us through enormous collections of two hundred year old plant specimens and international art exhibitions, through collaborations with a paleogenomics lab, a smell researcher, and a multidisciplinary artist, and through lots […]

]]>Could we bring back the smell of an extinct flower? Five years ago, this question started us off on an unexpected adventure that’s led us through enormous collections of two hundred year old plant specimens and international art exhibitions, through collaborations with a paleogenomics lab, a smell researcher, and a multidisciplinary artist, and through lots of cutting edge synthetic biology. The culminating immersive installation where you can smell the lost flowers, titled Resurrecting the Sublime, in collaboration with artist Dr. Alexandra Daisy Ginsberg, smell researcher and artist Sissel Tolaas, and with the support of IFF Inc, has been shown at a number of art museums in Europe and will be having its US debut this week as part of Nature—the Cooper Hewitt Design Triennial opening May 10 in New York.

This short film tells the story of Resurrecting the Sublime, from the herbarium to the lab to the art gallery:

A lot of people at Ginkgo and beyond have been involved in bringing this project to life, from the earliest explorations about whether it would be possible with Jason Kakoyiannis all the way through the first exhibition opening. In 2016 I visited the Harvard Herbarium with my former colleague Dawn Thompson on a mission to find extinct plants. Together, we combed the stacks for preserved specimens of plants from the IUCN extinction list. From the more than 5 million samples in the herbarium, we found about a dozen extinct specimens that we could take tiny bits of leaf from. We worked with the UC Santa Cruz Paleogenomics lab to uncover sequences of DNA involved in fragrance production, which our colleague Jue Wang stitched together electronically into two thousand different versions. A team led by organism engineer Christian Ridley used those sequences to build strains of yeast harboring the extinct DNA, and test engineer Scott Marr measured the lost scents each strain made.

We focused our attention on three plants:

The Hibiscadelphus wilderianus Rock, or Maui hau kuahiwi in Hawaiian, was indigenous to ancient lava fields on the southern slopes of Mount Haleakalā, on Maui, Hawaii. Its forest habitat was decimated by colonial cattle ranching, and the final tree was found dying in 1912.

The Orbexilum stipulatum, or Falls-of-the-Ohio Scurfpea, was last seen in 1881 on Rock Island in the Ohio River, near Louisville, Kentucky, before US Dam No. 41 finally flooded its habitat in the 1920s.

The ‘Leucadendron grandiflorum (Salisb.) R. Br.’, the Wynberg Conebush has a more complex story, which we are still uncovering. It was last seen in London in a collector’s garden in 1806; its habitat on Wynberg Hill, in the shadow of Table Mountain, Cape Town, South Africa, was already lost to colonial vineyards. This flower may prove to be completely lost: the project is bringing to light that specimens around the world may historically have been incorrectly identified.

Once we had the list of molecules that the extinct DNA sequences were making in our yeast, we worked with smell researcher Sissel Tolaas to compose those molecules into a complex smell. Sissel used her deep expertise in chemistry and smell to reconstruct the flowers’ smells in her lab, using identical or comparative smell molecules to what we measured in the foundry. Smelling Sissel’s sketches for the first time was magical and uncanny—we were smelling something impossible.

In large scale immersive installations designed by Daisy Ginsberg, fragments of Sissel’s smells diffuse through the air. As you smell the extinct flower and experience the geology of the lost landscape, you become part of an inverted natural history display—the human is the specimen on view.

Resurrecting the Sublime at the St. Etienne Design Biennial. Photo credit: Pierre Grasset.

For me as a biologist, art has been a really important way for me to ask questions and explore the many facets of biotechnology and its place in society. For extinctions that were caused by the actions of humans, asks us to contemplate our actions, and potentially change them for the future. I’m so thrilled to have been able to collaborate with so many brilliant scientists and artists on this project. The experience has been truly sublime. For more info, check out resurrectingthesublime.com.

Day in the Life of Software, Whimsy, and Danhttps://www.ginkgobioworks.com/2019/04/01/day-in-the-life-dan/
Mon, 01 Apr 2019 15:18:01 +0000https://www.ginkgobioworks.com/?p=3384As a part of our “meet the Ginkgo team” series, today we’re featuring a chat with Dan Cahoon, a software engineer (or, software Jedi). Curious how a software engineer ends up working in biology? Read on: Tell us a little more about your background and what brought you to Ginkgo: I was a chemistry and […]

As a part of our “meet the Ginkgo team” series, today we’re featuring a chat with Dan Cahoon, a software engineer (or, software Jedi). Curious how a software engineer ends up working in biology? Read on:

Tell us a little more about your background and what brought you to Ginkgo:

I was a chemistry and biology major in college – but I ended up taking some computer science classes my sophomore year because they counted toward my major. Those ended up being my favorite classes, and I soon figured out I liked coding more than I liked being in the lab, so I went on to minor in computer science. After graduation I was looking for jobs that could combine biology and computer science. Someone in my lab had met one of Ginkgo’s founders (Jason) and connected us, and I’ve been at Ginkgo ever since.

I’ve actually been at Ginkgo longer than anyone besides the founders; they gave me the chance to develop my skills, and believed in me from the start so I could really hit the ground running and apply my biology knowledge to work on some pretty fascinating problems.

What’s your high-level impact at Ginkgo?

It has changed a lot over the years but in short: to make biology easy to engineer, you have to be able to create repeatable engineering experiments. That requires scaling up beyond what you could normally do with just a person working on their own. So I work with our sample tracking system to track what happens in the lab and enable robotic automation and automated data analysis. That process gives our organism engineers superpowers: they can do 1,000 times as many experiments as they would with manual processes.

What’s your typical day like?

I bike into work, and my first task is to sit down in our design studio and code for a few hours. After lunch I’ll have planning meetings or one-on-one check-ins with team members to make sure they’re making progress, have a good idea of what they should be doing and how to do it, and most importantly that they’re happy. We’ll cover things like backlogs and priorities so we can figure out how long various projects will take and commit to getting features rolled out in a timely manner.

Right now my team is creating a link between our sample tracking software and a new automation software, so that we can capture what’s happening on our robotic platforms and not have to manually enter all that information. We’re also building the front end to allow users to specify what their experiments are and then run them on our robotic automation platform.

What’s the most unique part of your day-to-day?

Aside from the software developer side of things, I’m the “Chief Whimsy Officer” at Ginkgo. The role is really about ensuring that we’re having fun while we tackle some really important problems. Creating a culture of whimsy lets people be comfortable coming to work as themselves, and encourages a happy and safe environment. If people are engaged in their work and feel they can express themselves, they will be better at their jobs and be more productive. It’s just common sense: if somebody is miserable they’ll do the bare minimum. But if you know your day is going to be fun, you’re going to want to show up and do your best work.

I help make sure we’re doing silly things like holding “whimsy office hours” where we can play VR games and make new Slack emoji. I try to allocate some time out of every week for things like this, because it’s a big part of Ginkgo’s culture to be silly and whimsical. My dream is to run a model train between the foundries to deliver plates of samples around. It’s a system we do need, but I like the idea of bringing in a whimsical touch.

Again, being a software developer at a biology company seems pretty unique. How would you explain your job to other developers?

We’re still serious engineers. Ginkgo is using a lot of cutting-edge developer tools, like React and GraphQL and our developers write Ruby, Javascript and Python. Our software stack has grown tremendously because all our developers are encouraged to evaluate new tech and bring it on board.

At the same time, it’s unique because we’re working on some really powerful science, doing things that have never been done before, and being a part of that is incredible. At Ginkgo, you’re working on something that’s going to change the world, which is more interesting than programming for adtech or changing Google’s search algorithm to be slightly faster. Those things are important, but can’t compare to terraforming Mars with synthetic biology or bringing back the scent of an extinct flower. There’s nowhere else in the world where things like this are happening on a daily basis, and knowing Ginkgo’s incredible work is propelled by the software I wrote is the greatest part of my job.

]]>Introducing Motif: The Future of Food is__________https://www.ginkgobioworks.com/2019/02/26/introducing-motif/
Tue, 26 Feb 2019 13:47:01 +0000https://www.ginkgobioworks.com/?p=3299When people talk about the future of food, they often start by talking about how the human population is projected to reach 10 billion people by the year 2050. To feed a rapidly growing population with an expanding middle class on a warming planet, we’ll have to use new technologies and build new systems to […]

]]>When people talk about the future of food, they often start by talking about how the human population is projected to reach 10 billion people by the year 2050. To feed a rapidly growing population with an expanding middle class on a warming planet, we’ll have to use new technologies and build new systems to grow and distribute food. But whether it’s about choosing our next meal or feeding a growing population, the stories we tell about the future of food are full of impossible tradeoffs between taste, cost, health, and the environment (think Soylent vs. Whole Foods). And when it comes to GMOs specifically, the tradeoff is even more stark. Will it ever be possible for food be sustainable, healthy, delicious, and affordable?

At Ginkgo, we believe that biotechnology is an essential part of the future of food, and we hope that it can give us more options, not fewer. We’re working towards a future where genetic engineering and cultured ingredients can help make foods that are more sustainable, healthier, delicious, and more accessible for everyone. It’s what drives our work with customers in the flavor & fragrance and food industries to make cultured ingredients and the work of Joyn Bio, our joint venture with Bayer engineering microbes for more sustainable agriculture.

Today we’re thrilled to be launching Motif Ingredients, a new company built on Ginkgo’s platform to address one of the biggest challenges and changes emerging for the future of food—protein. Recognizing the benefits to health and sustainability that come from a plant-based diet, consumer demand for complements to animal proteins has exploded in the past few years, for products ranging from oat milk to “bleeding” veggie burgers. Companies ranging from brand new startups to industry giants have rapidly innovated new foods based on alternative proteins, but there’s so much more to do to make these options as healthy, delicious, sustainable, and accessible as they should be. Motif Ingredients will use Ginkgo’s Foundry to discover and develop these necessary new alternative protein ingredients that can be made via fermentation, not animal agriculture.

Motif Ingredients is launching today with $90M in Series A funding from Breakthrough Energy Ventures, Fonterra, Louis Dreyfus Company, and Viking Global Investors. Our investors come from both high tech venture capital and traditional food producers that have been feeding the world for more than a century, all believing in our platform’s ability to deliver more alternatives for everyone’s “food future”. Motif will operate from Ginkgo’s offices in the Boston Seaport and leverage our foundries to discover the next generation of alternative proteins. We’re also excited to welcome industry veteran Jon McIntyre to the team as Motif’s CEO. Formerly the head of R&D at Indigo Ag and prior to that, a Senior VP of R&D at PepsiCo, Jon brings a wealth of experience in global food systems and alternative proteins to Motif.

A platform for discovering the next generation of food proteins

Proteins in animal products like meat, dairy, and eggs are essential for the taste, texture, nutrition, health impact, and overall experience of many foods that we eat. Food proteins have unique structural and functional properties, whether they are egg proteins giving a dessert its fluffy texture, or milk proteins protecting a baby’s digestive system from dangerous bacteria. Motif will make different proteins like these via fermentation of engineered microbes, without animal agriculture, to create a rich palette of alternative protein ingredient options for people developing new foods.

An introduction to Motif’s technology by Karen Ingram

Ginkgo’s platform enables biological engineers to deeply study thousands of different protein options across a vast space of biological diversity, discover the proteins that provide the greatest functional benefit, and increase their accessibility at large scale. There is so much that we don’t yet know about even the most common foods, so the ability to search this breadth of biological diversity is essential. Even in the last 5 years, hundreds of new proteins have been discovered in milk and eggs that confer benefits to people who eat them. With Motif, we’re on a mission to explore all that animal proteins have to offer, to enable the next generation of alternative proteins.

Beyond cow’s milk and hen’s eggs, there are also foods with vital benefits that are impossible to access in large amount sustainably, such as sturgeon eggs, camel milk, and everything in between. Just one year ago, scientists discovered a new protein in platypus milk that has surprising antibiotic properties. Using DNA sequence analysis and synthesis, Motif’s scientists will be able to discover and produce hundreds of proteins from many different animals, to understand how their milk and eggs nourish and sustain life in its earliest stages and identify important new ingredients.

At Ginkgo, we are always learning from the creativity of biology and the full breadth of biodiversity to grow better, more sustainable products. We’re so excited to work with Motif as they look to biodiversity to find the proteins that will enable new creativity in food. We’re thrilled to welcome Motif to our platform and to support the next generation of chefs, food designers, and food visionaries who need new ingredients and tools for the future of food.

]]>Nature of Sensing: Reflections on the 2018 Ginkgo Creative Residencyhttps://www.ginkgobioworks.com/2019/02/05/2018-creative-in-residence/
Tue, 05 Feb 2019 16:01:19 +0000https://www.ginkgobioworks.com/?p=2787Beyond Vision, Sensing Takes on the Physical Working in hardware and software for the last decade has opened up my curiosity and interest about sensors and what they have enabled our everyday inanimate objects to be. Embedded in our everyday devices, these sensing bits create layers of information to interact with. While sensors continue to […]

Working in hardware and software for the last decade has opened up my curiosity and interest about sensors and what they have enabled our everyday inanimate objects to be. Embedded in our everyday devices, these sensing bits create layers of information to interact with. While sensors continue to become smaller and faster, the limitations for the types of interactions they provide remain limited. When we look at human sensing capabilities, it is quickly apparent that our sensory interactions with the world span far beyond vision. We can smell, taste, sense proprioception, comprehend ambiently, sense peripherally and in a group. When I look outside of the human and turn to other living things — the plants and insects I see on a hike in the California desert, the microorganisms in my fermented foods, my neighbor’s cat who wanders in the neighborhood – I see how crude our sensing technologies in hardware and software are. Comparing a car to termites reminds me to stay humble.

At the molecular level, how do living things sense and interact with the chemical world? The foods and toxins that organisms are attracted to and repelled from? Smells, flavors, hormones are chemicals. They are molecules occupying space. Sensing these molecules is a physical interaction, and biology becomes crucial aspect of that design, uniquely able to detect molecules with incredible sensitivity and precision. I began my residency with this frame of mind.

Yasaman Sheri in the Cold Room in the Ginkgo Bioworks Foundry.

A Biosensor Anthology | Making the Invisible Visible

Biosensors are invisible to the naked eye. Because their scale is so small, they require scientific apparatus to view, capture, and interact with. I made it an important part of my process to learn from the scientists at Ginkgo by listening and sharing my way of understanding as we used different language and terminology to communicate similar ideas. To my surprise, the language around software was easily understood and provided a parallel in the two fields of computing and synthetic biology:

inputs / outputstrigger / feedbacksensing / reacting

While I am critical about the cross over of metaphors from computing to biology, I found it a fast way to build trust and communicate clearly with the experts. Through what felt like endless conversations with scientists and engineers at Ginkgo, I compiled a BioDesign Dictionarya place where I would store new terminology I came across.

As I began to list, write and research, I discovered that most often biosensors are proteins that sense a chemical molecule. Although there are other types of biosensors that sense physical changes such as pressure, changes in the cell wall, or movement, I decided to focus on biosensors that can detect chemical molecules.

“If there is a chemical in nature, there is a biosensor for it in nature.”

-Ginkgo’s Head of Selections and Strain Improvement, Nikos Reppas

The notion of learning from nature and designing new biosensors is powerful, however it doesn’t mean it is possible to do so in a matter of months. I began to explore the scientific literature, and learned to work with biosensors that Ginkgo engineers used in the foundry. As I collected scientific papers and worked with the Ginkgo scientists, I built an inventory of biosensors, a short taxonomy from a perspective of a designer who is interested in sensing.

Abstract visualization of a protein biosensor in the 3D software PYMOL.Front view of TRPA1 Itch Sensor. The geometry and the shape of the surface defines the sensing.A short anthology of various biosensors and their typological shape responsible for sensing. PyMoL Mesh. Design by Yasaman Sheri.

The way a protein and molecules senses the presence of each other is by fitting in to one another, physical contact, like a key and lock. Sensing in this case means for a molecule to fit into a protein; the geometry and topology define the interaction.

“The geometry and topology define the interaction.”

Inspired by the apparatus that scientists use to view, modify and ultimately work with proteins, I wanted to interact myself with these invisible things. I learned basics of PyMol software and worked with the scientists in protein engineering teams to give form to the intricate topological shapes that so defined the sensing. Although this exercise felt more like gathering and collecting, it helped me understand how detailed and unique each sensor is.

Paper as Interface | Material Intelligence

I strived to embody biosensors in a medium that is familiar. I researched various materials and found that paper was interesting to work with for several reasons. Paper absorbs water – in life sciences, water matters. Paper can be flat packed and shipped. Paper is lightweight and affordable. Paper comes in variety of colors, thicknesses, and textures. But more than its material properties, paper has cultural and scientific historical significance that felt relevant in sensing and perception. Paper is a material we have used to sketch ideas on, externalizing our imagination. Paper is used to write on, to embed knowledge, to carry our ideas, instructions, stories, and agreements. Paper serves as a cultural vessel that builds societal exchanges of thought. From a scientific historical perspective, paper has a legacy for “sensing”. Paper has been used as a tool for diagnostics, disease detection: Universal pH Tests, Urine Tests, and Pregnancy Tests.

Universal pH Sensor | Paper Diagnostic | Photograph by Yasaman Sheri

Experts in paper based biosensing diagnostics, Keith Pardee and a team at the Wyss Institute for Biologically Inspired Design at Harvard have been working on cell-free methods to embed genetic machinery in paper, including biosensors that can act as diagnostics or other useful low-cost sensing devices. The concept of cell-free sensors inspired me since it meant that there are no living organism, it enables me as a designer to take the paper embedded with biosensors outside of an enclosed laboratory. It also meant that to “activate” the sensing interaction it would require to “add water”.

While most paper diagnostics come in a form of of a strip, held on one side, dipped on the other, I was eager to explore new affordances and interactions in this space. And turned out, both Wyss Institute and Pardee Lab were excited about that as well. I made a trip to the University of Toronto to visit Keith and we discussed several ways I could work with paper and explore biosensing. I also visited the Wyss institute and talked to experts in synthetic gene networks and paper intelligence. In these visits I learned that with cell-free paper systems, physical contact was important. It is harder to sense molecules in air through paper.

Gaining knowledge in this area of intelligence, I began to prototype intricate affordances for wearable paper sensors. This was something I could sketch without embedding the sensors in, to explore interaction and form at the human scale.

Paper Sketches by Yasaman Sheri exploring interfaces for biosensing

Micro Organism with a Nose | Smell Biosensor

While sketching physical interactions and interfaces helped me explore ideas, I wanted to see biosensing in real time and in action. To do this, we embedded two different biosensors in living organisms. This was the fastest and easiest way for me to experiment with sensing biologically. One of my biggest findings has been that Lab work and Design sketching may have similarities in process, but they have very different spaces. I had to split my time between being in the lab with safety attire, and in the studio where I could sketch object interactions rapidly. Time scales in biology are wildly different than that of computing. Life takes time – living things sleep, eat, grow. And there are not that many shortcuts to accelerate that process than a few standard practices.

“Life takes time.”

I worked with Joshua Dunn, Ginkgo’s Head of Protein Design and Creative Residency Mentor, along with other scientists to create the microbial interaction. We worked with a strain of yeast that Ginkgo engineers designed to biofabricate and produce a unique aroma. We fed the yeast with food that it likes and after two days of incubation, it was able to produce the smell we had designed it to create. On the same Petri dish we grew a strain of E. coli harboring an olfactory biosensor, giving the bacteria the capability to smell — a “nose”, if you will. The smell biosensor would sense the presence of the odor we asked the yeast to produce.

What happens after sensing requires another tool and different biological mechanisms, called “reporters” which define the output. I was surprised to find that the reporters available were quite limited to a few outputs such as color and fluorescence. While it may be sufficient for a scientists to use these outputs to detect a microbial interaction with naked eye, from a design perspective it stays limited to visual perception. I am eager to evolve this area of feedback in biology to open up experimentation for unique interactions as diverse as sensing in future work.

On our microbial interaction petri dish, the E. coli was designed to “output” the color blue once it smelled the odor. On this plate, the two newly designed microorganisms — the odorous yeast and the sniffing E. coli — shared a sensing interaction.

E-coli with embedded biosensor turns blue on the left upon sensing the odour produced by yeast on the right.

Josh and I continued to work together to do several iterations and prototypes of our microbial- sensing experiments. Other prototypes included flavor biosensors, distance interactions between two micro organisms, and embedding the sensors on Watman paper.

Experiment in designing smell-producing yeast and its distance spatial interaction with E-coli bacteria on same plate. Yeast and e-coli grown at variable distances.

Museum of Sensing | Collective Sketches for Social Dreaming

As the field of biodesign matures and evolves, the area that I continue to find most interesting is the process of working with people from different disciplines. The creative process and the scientific process both need —just as bacterial growth— the right conditions to flourish: a supportive environment, good nutrition, plenty of water, etc. The conditions for sketching creative prototypes, ideation and futures for biology is one that allows for collaboration, ambiguity, and openness. The nutrition for sketching biology is passionate minds coming together, expression of what is an invisible idea in the mind to a visible sketch, be it physical, digital, flat, volumetric, interactive, or simply performed… when we can share our thoughts we allow the ideas to grow and take place in reality.

Hands on sketching with Scientists at Ginkgo Bioworks | Workshop led by Yasaman Sheri

I shared two different styles of thinking, Brainstorm and Design Critique. One, a judgement-free space that allows everyone of all backgrounds, ethnicity, seniority or position in the company to contribute and have a voice through making. We established that when we don’t criticize or judge the ideas at their infancy, we breathe into them an expression. The other, participants were encouraged to constructively share feedback with suggestions and considerations. This space was about gaining perspective, checking for bits overlooked, and also about diversity of experiences and thought. Our upbringing and the environments we are situated in often define our point of view and if we are designing for the greater world, then it is helpful to get perspective and feedback often, especially in a field that will affect not only humans but all parts of life. Here we had space to talk about why an idea is desirable and undesirable, why it is good and bad, why it might make me afraid or make me fall in love.

As we got in to groups and sketched ideas together, we practiced social dreaming. When we think about biological sensing, what do we want collectively on our planet? What do we expect in our communities and as individuals? What biosensors are desired? And what kind of sensing is undesired? Our hopes and fears take on a shape to be visible in this space.

One way to capture these sketches of biological designs was to put them in a museum. I gave each Ginkgo member a tag where they would write about their newly sketched tools and what it sensed. As they gave the tags back to me I stamped them “ARCHIVED”, officially confirming their contribution to “The Ginkgo Museum of Sensing”. From the objects they brought initially from their homes tagged as 2019, to the objects they sketched for 2039, Ginkgo scientists’ visions and ideas were documented in “context of their body” as wearable and later mounted at Ginkgo Bioworks HQ as a collective memory of the biosensors to come.

This sort of thinking about critique and questioning the how, why, and who of decisions made about new technologies is an important part of my work on sensing technology. When it comes to biosensors and what is designed, brought in to market and the data that is collected and measured, new questions beyond usability and technical feasibility arise: Who decides? how is it decided? and how does the idea evolves from sketch to the complex socio economic world that is never devoid of political boundaries, geographically or otherwise?

With Systems thinking and Platform Design in mind, I wish to share my knowledge and open up biosensing technologies as tools of expression, connection and communication. My time in the lab working with scientists at Ginkgo Bioworks, opened my eyes (and senses!) to working with some of the world leaders in biosensing and helped me dive deeper in this emerging field to recognize the opportunities and challenges first hand.

Three months not only flew by, but it felt like an intro to biosensors, a taste of working at the biological time scale and with living systems of nature that we are still understanding and learning to not use, but work with.

The most profound exercise at the residency was not focusing on design, or science, but rather at the in-between space that cultivates both. My terminology is now: Sketching in Biology, Brainstorming Ecology, Designing Lab Experiments. These grey areas provide potential for multiplicity of viewpoints, and nurture a collective thinking about the future. It’s a hazy border that cultivates healthy disagreements and ways to come to understanding, one that involves humans and other species and opens the door for plural thinking in design and science and ecology.

]]>Day in the Life: Chrishttps://www.ginkgobioworks.com/2019/01/10/day-in-the-life-chris/
Thu, 10 Jan 2019 18:40:04 +0000https://www.ginkgobioworks.com/?p=2203In the latest edition of our day-in-the-life series, we hear from Chris Mitchell, Software Engineer about his journey to the engineering team at Ginkgo Bioworks. How did you become involved in your industry and what led you to work with Ginkgo on the software engineering side? I actually don’t have a formal education in computer […]

]]>In the latest edition of our day-in-the-life series, we hear from Chris Mitchell, Software Engineer about his journey to the engineering team at Ginkgo Bioworks.

How did you become involved in your industry and what led you to work with Ginkgo on the software engineering side?

I actually don’t have a formal education in computer science. I earned my Ph.D. in Biochemistry, Cellular and Molecular Biology from Johns Hopkins and I’ve been a self-taught programmer since the age of 16. Throughout my academic career in the sciences, I spent a lot of time in the lab and became closely acquainted with the huge amount of data and repetitive manual tasks that come with running experiments. For me, software was the perfect way to bridge two worlds I was closely ingrained in to solve some major inefficiencies I was experiencing first hand in the lab. I landed at Ginkgo after someone from the company found my GitHub page and saw some of the tools I was building – new analytical tools for mass spectrometry and sequencing data, as well as a project to enable reproducible data science. After meeting the team at Ginkgo, I was blown away at how quickly they understood the nuances of my work and the caliber of the team. So began my formal entry as a software engineer in the life sciences.

Tell us a little about your role and the impact you have at Ginkgo.

On a fundamental level, Ginkgo could not exist if it weren’t for automation, and automation can’t exist without software. Thanks to the level of automation Ginkgo has brought to the lab, we’ve reached new heights in scale, iteration, data and reproducibility in the synthetic biology industry.

The software engineering team at Ginkgo works with people across a number of different areas, including product management, lab work, analytical pipelines, sales and more. Software is the underlying technology that allows our platform for organism design to operate at such a scale, so it’s essential that we are constantly communicating with every team to ensure things are running smoothly, we’re addressing bottlenecks quickly, and building for the future.

To illustrate how the engineering team’s work affects the larger mission at Ginkgo, I can share a little about one of the projects I’m working on right now. We’re currently working to find a better way for our different users to interact with sequencing data. Sequencing data is used at nearly every stage at Ginkgo: the DNA Fabrication team uses it to verify synthesized sequences, the Build team uses it to verify strain constructs, and the Test team uses it to understand how the transcriptome and other genomic elements contribute to a given phenotype. There are also other indirect users such as data scientists trying to build models to improve future engineering efforts.

Thus, we have a diversity of users – some work with 10,000 samples and some only work with 3-4. It’s really challenging to build a UI and analytical capabilities that capture both ends of the scale in an accurate and consistent way but it is incredibly important. Users need to make informed decisions with as little margin of error. To enable that, we need to build software that permits quick, global insights into their data but also provides the ability to drill down to the most basic elements of a given data type. Users also need to be able to analyze and refine parameters
without rerunning entire workflows that can take hours to complete.

Many people would probably be surprised to hear that you’re a software engineer at a biology company rather than a tech company – what’s that experience been like for you?

A common problem for any software is being built on legacy infrastructure that makes it hard to adapt as technology evolves. Luckily, Ginkgo’s founding team made some smart decisions early on about which stacks we’d build the technology on and we’re continuing to reap the benefits on the developer side. Since then, the leadership and culture at Ginkgo has continued to embrace change and as a developer, I feel empowered to explore and implement new technologies.

For instance, when I came to Ginkgo we were using VMs to run our applications and now we are entirely Docker-based. Similarly, all our UI development is now in React and GraphQL to stitch our data together. These choices have made it so we can standardize the developer experience in terms of spinning up services but still allow some exploration on the underlying tech stack. For example, we have microservices written in Ruby on Rails, Django, Node and Go, which largely were chosen on the basis that the language was the best suited for the particular microservice’s task.

On a more philosophical level, part of the reason why I love working on Ginkgo’s engineering team is that we are building an entirely new frontier. So much of today’s developer role is focused on making something run a half a second faster or increasing ad engagements by 2 percent. Instead, I get to apply those same frameworks and technologies to solve novel problems in synthetic biology, like how to predict the metabolic network for a piece of genetic code.

How have you seen the role of the developer evolve?

The biggest change I’ve seen over the years is a stronger desire from developers and engineers to want to leave a lasting legacy with their work. People in this industry are realizing the power and importance of the technology they work with and want to put those efforts toward bigger problems that can change the world. You’re starting to see developers looking for opportunities where they can have a larger impact and applying their skills to solve big problems in healthcare, sustainability, autonomous vehicles and more.

]]>Day in the Life of Dawn and NGShttps://www.ginkgobioworks.com/2018/10/17/dawn-head-of-ngs/
Wed, 17 Oct 2018 17:25:43 +0000http://www.ginkgobioworks.com/?p=2045 Today, in our series exploring the day-to-day lives and interests of Ginkgo employees, we talk with Dawn Thompson, Head of Next Generation Sequencing and Senior Biological Engineer at Ginkgo. How did you become involved in your industry? Tell us a little bit about your background and the path that brought you […]

Today, in our series exploring the day-to-day lives and interests of Ginkgo employees, we talk with Dawn Thompson, Head of Next Generation Sequencing and Senior Biological Engineer at Ginkgo.

How did you become involved in your industry? Tell us a little bit about your background and the path that brought you to Ginkgo.

I’m a biologist primarily because I love understanding how things work. I’m a geneticist, with the bulk of my training in genomics. The most exciting thing about genomics to me is understanding how the DNA in your genome gets translated into particular characteristics, and how the contents of your genome can be decoded to determine what makes you, you. Of course, people are really complicated, from a DNA perspective, so the simplest way to practice genomics is to look at a simple organism. That’s why I decided to focus on microbial biology. Microbes are fascinating; they live everywhere on the planet — glaciers, volcanoes, even on us — and they do all these fantastic things.

When I was just starting out as a geneticist in graduate school, I was studying one gene at a time, but I knew to really work in genomics I would need to understand entire genomes. I joined the Broad Institute, an arm of MIT and Harvard that was launched in 2004 to improve human health using genomics, and worked there for 9 years studying genomes and their characteristics.

I loved my time at the Broad Institute, but every 10 years or so, I like to look at my career and think: What other cool stuff is there to learn in biology that I haven’t explored yet? To me, synthetic biology was the obvious next step. Synthesizing DNA was getting cheaper, as was sequencing, meaning we could now both “write” (synthesize) and read (sequence) genes in a cheap, high-throughput way. That opened up all kinds of ways to use synthetic biology to understand the functions of cells and program them to serve new functions.

Ginkgo Bioworks was the perfect opportunity to explore synthetic biology and combine my interest in microbes, my expertise in evolution and genomics, and my passion for understanding how things work on a biological level. This August, I’ll be celebrating three years there, leading out next generation sequencing team.

Tell us a little about your role – what’s the high-level impact you have on Ginkgo?

Ginkgo is divided into two primary departments, foundry teams and customer-facing teams, and as part of my role as a senior biological engineer I’m involved in both sides of the business.

My primary responsibilities are on the foundry side, providing services and support for internal Ginkgo teams and helping our organism engineers determine which of our organism designs are working the best. To do this, my team and I leverage Ginkgo’s next generation sequencing platform (which I played a primary role in creating), allowing the organism engineers to sequence the constructs they use in their organism engineering and sequencing those organisms so that the engineering teams can understand their genomic sequence and ultimately design them.

My team is about 10 people right now, a mix of scientists handling the gene sequencing and bio-mathematicians who can analyze the resulting data.

Photo Credit: Tim Llewellyn

When Ginkgo takes on a new project, we often have a new microbe that we want to work in. My team is one of the first steps in that process. We call it “onboarding a new host organism.” Typically, we can design something on the computer and understand what the sequence will be. But in order to do that, you need to first understand the full genomic sequence of an organism. So for new host organisms we’ll do a custom project where we do several types of sequencing, a lot of computational analysis and then generate what’s called the “reference genome” for them. It’s a really collaborative process.

A real benefit Ginkgo — and our team specifically — offers to our internal engineers is that, because of our next generation mix of automation, we can do all of this in high throughput work cheaply and quickly, speeding up the overall engineering cycle and get answers fast.

Photo Credit: Tim Llewellyn

What’s most exciting to you about the work Ginkgo is doing right now?

Our new agtech company Joyn is super cool. About 15 years ago I was trying to figure out my career, and was fascinated by the idea of going out in the field to sequence organisms in the oceans and soil. Now that’s actually some of the work we’re doing with Joyn as we try to figure out how to engineer a microbe that can live in the soil and help plants grow, replacing nitrogen fertilizer with a more “green” process.

Our tagline is, we’re trying to make biology easier to engineer. In order to do that, we need to understand biology better — and identify the common themes and designs that will help speed up our process.

That will allow us to replace a really labor-intensive, expensive, resource-demanding process with something very green. You can make a lot of stuff both cheaply, and not use a lot of resources that create problems with waste that you need to dispose of. Biomanufacturing is a very cool green process.

Mother nature is the best engineer! If we source all the biodiversity in nature and understand what’s in the genomes in those organisms, it opens up a wide range of functionality. Ginkgo is well on its way to demonstrate that this is a technology that is not only here to stay but can be leveraged to create anything — to make textiles, to replace plastics. If we do it right, we don’t need petroleum based plastics anymore!

Photo Credit: Tim Llewellyn

What do you love most about your job?

It’s hard to pick just one thing, but one of the things I love the most about my work at Ginkgo is that we are using state-of-the art methods to interrogate so many aspects of cellular function. Our sophisticated automation allows us to do this at scale, taking a holistic approach to organism engineering. This is a powerful and versatile way to create organisms for our customers; the resources at Ginkgo allows us to interrogate biology in a way we haven’t be able to previously. We can understand biology on an entirely new level and in turn identify common themes or design principles that can be then be used for a wide variety of applications. It’s almost limitless.

]]>Cultured Cannabinoidshttps://www.ginkgobioworks.com/2018/09/04/cultured-cannabinoids/
Tue, 04 Sep 2018 11:59:30 +0000http://www.ginkgobioworks.com/?p=1988Cannabis is a fascinating and rapidly growing industry, predicted to reach $57 billion worldwide by 2027. As legalization spreads, so too does our understanding of the potential benefits of the many different molecules present in the plant. Beyond the better known THC and CBD, cannabinoids present in tiny quantities in the plant have the potential […]

]]>Cannabis is a fascinating and rapidly growing industry, predicted to reach $57 billion worldwide by 2027. As legalization spreads, so too does our understanding of the potential benefits of the many different molecules present in the plant.

Beyond the better known THC and CBD, cannabinoids present in tiny quantities in the plant have the potential to be valuable in a range of pharmaceutical applications. Ongoing research has shown potential medicinal uses for indications such as chronic pain, nervous disorders, nausea, weight loss, and some mental illnesses.

But to unlock the value of these molecules, we first need to be able to access them. Today we’re announcing a partnership with Toronto-based Cronos Group to produce a range of different cannabinoid molecules through fermentation of engineered yeasts. It’s a large-scale and long-term deal, involving up to $22M for R&D along with a total of up to $100 million worth of Cronos common shares upon achieving pilot commercial scale.

The Science:
There are hundreds of different cannabinoids produced by different varietals of the plant. Long term breeding has led to strains that produce large amounts of THC(A) and CBD(A) (the A stands for acid, a different chemical form that is converted to THC and CBD when heated) but other molecules such as CBC, CBG, and THCV are present only in trace amounts, meaning that they are impractical or impossible to extract and purify from the plant. Without a cost effective supply, research into the pharmaceutical properties of these molecules has also been hampered. THCV, for example, has been shown at low doses to offer relief from anxiety without the appetite stimulating effects of THC, but so much is still unknown.

By transferring the DNA sequences for cannabinoid production into yeast, using the foundry and our existing high-throughput fermentation processes, we’ll work to construct strains that produce a range of different cannabinoids at high quality and purity, identical to those extracted from the plant with traditional methods. By capitalizing on the power of biological manufacturing, we can unlock access to medically important cannabinoids that can be scaled up and produced reliably.

Why Cronos:
We’re so excited to be working with the Cronos Group on this landmark partnership. Cronos, based in Canada and with a presence across four continents, is a vertically integrated cannabis company that operates two licensed producers regulated under Health Canada’s Access to Cannabis for Medical Purposes Regulations. Cronos, with access to an array of varietals and a deep expertise in plant genetics, has gathered extensive data on cannabinoids and their properties. This allows them to generate the best recipes for the full spectrum of cannabinoids, not just the most common ones.

We’ll be working to develop strains of yeast that can produce eight different cannabinoids. All the R&D work we’ll be doing at Ginkgo will of course be conducted in compliance with all U.S. federal laws regarding controlled substances, and we’re currently waiting for approval from from Federal and State agencies. Cronos Group intends to produce and distribute the cultured cannabinoids that result from our partnership globally, and has received confirmation that this method of production is permitted under the Cannabis Act—the legal framework that will regulate cannabis in Canada.

As Ginkgo has grown, we’ve seen the power of biological engineering and fermentation to unlock the potential of a huge variety of molecules in several industries, from flavor and fragrance to pharmaceuticals. We’re thrilled to be working with Cronos as they build the world’s most innovative cannabinoid platform to bring these products to life.

]]>Our 2018 Creative Residenthttps://www.ginkgobioworks.com/2018/08/23/our-2018-creative-resident/
Thu, 23 Aug 2018 11:25:00 +0000http://www.ginkgobioworks.com/?p=1979We’re so excited to announce that Yasaman Sheri will be joining us as our second Creative Resident this fall! Yasaman is a designer exploring the potential for interactions beyond the visual interface, through augmented and virtual reality, sensory, and other biological systems. Yasaman’s career has spanned many fascinating technologies and systems. She was one of […]

]]>We’re so excited to announce that Yasaman Sheri will be joining us as our secondCreative Resident this fall! Yasaman is a designer exploring the potential for interactions beyond the visual interface, through augmented and virtual reality, sensory, and other biological systems.

Yasaman’s career has spanned many fascinating technologies and systems. She was one of the first designers on the original Microsoft Hololens Operating System team, where she led design interactions on Windows Holographic for five years and designed novel spatial and gestural interfaces for augmented and mixed reality.

Since her time at Microsoft, Yasaman’s research and design work has focused on leveraging her knowledge in machine sensing to expand human experience of sensing and perception. Working with companies like Mozilla, Toyota, and Google X, and teaching at the Copenhagen Institute for Interaction Design and Art Center College of Design, she’s built a unique understanding of sensory design beyond the visual, extending into smell, taste, and haptics.

Student work from Yasaman’s Sensory Design course at the Copenhagen Institute of Interaction Design (header image above is from the same project)

Sensing the environment is fundamental to living things, whether bacteria sensing the gradients of chemical resources in their watery surroundings, snakes sensing the heat of their prey to “see” in the dark, or humans smelling a delicious meal simmering in the kitchen. Biosensors are also fundamental to the study of biochemistry and the practice of synthetic biology: our earliest understandings of gene expression come from studying the system that the bacterium E. coli uses to sense and respond to the presence of lactose sugars, which in turn is used every day in labs to control the function of synthetic gene circuits.

During her time at Ginkgo, Yasaman will explore the design of biosensors in synthetic biology and their potential for intersection with human interaction, bringing her expertise as a designer of sensory experiences and interactive interfaces to this world of biosensors. We’ll be sharing updates from her time at Ginkgo here on the blog and on the Ginkgo Creative Residency Instagram @ginkgocreativeresidency.

]]>Our work on biosecurityhttps://www.ginkgobioworks.com/2018/06/26/our-work-on-biosecurity/
https://www.ginkgobioworks.com/2018/06/26/our-work-on-biosecurity/#commentsTue, 26 Jun 2018 08:50:16 +0000http://www.ginkgobioworks.com/?p=1871Our mission is to make biology easier to engineer—that hasn’t changed for the ten years we’ve been building Ginkgo. The ability to read, write, and design DNA code is having profound positive impacts in medicine, agriculture, and manufacturing, from engineered cell therapies that can target a person’s cancer cells, to probiotics for plants that can […]

]]>Our mission is to make biology easier to engineer—that hasn’t changed for the ten years we’ve been building Ginkgo. The ability to read, write, and design DNA code is having profound positive impacts in medicine, agriculture, and manufacturing, from engineered cell therapies that can target a person’s cancer cells, to probiotics for plants that can reduce the need for nitrogen fertilizers, to sustainably grown materials.

We are working to unlock the enormous power of biology: its ability to grow sustainably, to process information, and adapt to changing environments. But we’re not naive to the potential risks. We understand that as it becomes easier to engineer biology, it will become easier to engineer the part of biology that’s dangerous to humans, animals, and plants—the pathogens and parasites that can infect us. Since researchers synthesized the polio virus in 2002, it has been technically possible to chemically synthesize viruses that infect humans

To date, the work done on synthesizing viruses has been intended for medical research and other peaceful purposes, but there is a concern that someone could theoretically produce a virus or other pathogen with the intent to harm. The intentional use of pathogens to harm others is abhorrent and something that I believe that we should never do under any circumstances—as a company and as human beings. The international community agrees with me on this: 180 countries including the United States are parties to the UN Biological Weapons Convention, which was first signed in 1972 and states that we are “never in any circumstance to develop, produce, stockpile, or otherwise acquire or retain: Microbial or other biological agents, or toxins…that have no justification for prophylactic, protective or other peaceful purposes.”

Today we’re announcing Ginkgo’s biosecurity initiative that directly addresses some of these potential threats from engineered DNA sequences. Our current work on biosecurity focuses primarily on detecting potential threats using software that analyzes DNA sequences.

As part of IARPA’s (the Intelligence Advanced Research Projects Activity) Fun GCAT program, we are developing software to monitor DNA synthesis. This software is intended to ensure that no one orders DNA sequences that could have a pathogenic function. Think of this like a malware detector in computer programming—“programs” being written in synthetic DNA will go through the detector software, which will flag any sequences of concern before they are synthesized. The custom software we’ve developed for designing DNA sequences in our foundries is a useful start for a project like this—we need to be able to predict the function of enzymes based on their sequences in order to design new functions in our engineered microbes. Rather than predicting if an enzyme sequence could be used to produce, say, a fragrance or vitamin, here we’re applying the same types of algorithms to predict whether a given bit of code could be potentially harmful.

Unlike computer viruses, however, new biological viruses can also evolve in the wild. When a new virus emerges, researchers quickly sequence it to understand where it came from and how to best treat it and develop vaccines against it. We’re addressing this as part of another software-based biosecurity initiative, IARPA’s Finding Engineered Linked Indicators (FELIX) program. Here we are using deep learning to identify if the sequence of a new pathogen developed naturally or was engineered by humans. We’re leveraging our experience engineering the world’s largest library of engineered DNA sequences to help us train the software to detect whether something has been engineered.

Beyond developing software to guide the detection of threats, synthetic biology can also be important for responding to emerging diseases, for example making rapid response vaccines. It’s been almost a decade since the Venter institute partnered with Novartis on rapid synthetic DNA based vaccine development and the technology has been exponentially improving since then. Working alongside other companies, universities, and government agencies, we’re excited to be part of groups involved in developing tools to prevent, diagnose, and treat current and emerging diseases.

Ginkgo is the leading developer of genetic engineering tools we have an obligation to ensure that these tools are responsibly used. We are inspired by the words of Andy Weber, the former Assistant Secretary of Defense for Nuclear, Chemical & Biological Defense Programs under President Obama and a valued advisor to us here at Ginkgo on issues of biosecurity: we believe that while synthetic biology may lead to new risks, that these new tools also actually “offer the opportunity to take the global threat of biological weapons off the table.” By helping to develop software that can detect any threats before they materialize and develop the tools that can rapidly respond to emerging infectious diseases—natural or engineered—we hope to continue to drive the responsible growth of synthetic biology and realize its enormous potential for good.

]]>https://www.ginkgobioworks.com/2018/06/26/our-work-on-biosecurity/feed/7Celebrating iGEM + Ginkgo Historyhttps://www.ginkgobioworks.com/2018/06/15/celebrating-igem-ginkgo-history/
Fri, 15 Jun 2018 12:02:40 +0000http://www.ginkgobioworks.com/?p=1862We are so thrilled to be announcing a new partnership with iGEM (the International Genetically Engineered Machine competition). As sponsors, we’ll be supporting iGEM’s future growth and the growth of the community of synthetic biologists that they have built. The connections between Ginkgo and iGEM go deep. Tom Knight was one of the original founders […]

]]>We are so thrilled to be announcing a new partnership with iGEM (the International Genetically Engineered Machine competition). As sponsors, we’ll be supporting iGEM’s future growth and the growth of the community of synthetic biologists that they have built.

The connections between Ginkgo and iGEM go deep. Tom Knight was one of the original founders of iGEM when it was an intersession (IAP) class at MIT in 2003, along with Randy Rettberg, Drew Endy, and Gerry Sussman. Austin and Reshma took part in the first class, where they worked on designing oscillating logic devices.

The first summer program version of iGEM was in 2004, and I was on the MIT team along with Jason and Tom. The project was to build synchronized chemotactic oscillators (which may still be impossible—youthful optimism!), though one tiny part of that of that project eventually grew into the publication of the first datasheet for a standard biological part.

The MIT iGEM team, summer 2004

In 2006 all the Ginkgo founders along with our Head of People, Samantha Sutton, were advisors to the MIT iGEM team. Our project was Eau d’e coli: E. coli engineered to smell like wintergreen and bananas. In many ways, Ginkgo’s eventual work in the fragrance industry traces back to this project!

MIT iGEM 2006 Live Demo of Eau d’e coli

iGEM is one of the most important organizations in the field of synthetic biology, building a vast and open community of students and mentors that are committed to building synthetic biology according to their strong values in openness, responsibility, and fairness. iGEM is also a vital educator of synthetic biologists—10% of Ginkgo has participated in iGEM as a student participant, advisor, or judge (iGEM students and others, see open job postings here!). We’re so happy to be supporting iGEM and excited to be part of building the future of synthetic biology together.